Great collaboration! 📠+🧬 Experiments and ML go hand-in-hand. Hopefully more to come in the future!

"Our findings argue against a strict reg. role for TAD boundaries in controlling gene expression [...] TADs appear to serve primarily to organize chrom. topology at a global scale"- taking it as support from the '3Ders' for my love of TFs as prime regulatory suspects😉 www.biorxiv.org/content/10.6...

We just released IRIS (7+yrs project), a tech we believe will transform cell biology by pairing high-resolution cell images with matched #scRNAseq, letting us interpret cellular form by its molecular ground truth. Huge tx to @JohannesBues, @JoernPezoldt, @CamilleLambert et al. shorturl.at/zgY8Z

Very much into this! "Future work will clarify the biochemical basis for how promoter-proximal elements, like SRR2, synergize with distal enhancers to support cohesin-independent long-range regulation."

Now that I'm settled in at @umasschan.bsky.social, I'm hiring at all levels: grad students, post-docs, and software engineers/bioinformaticians! The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.

While over here discussions are about slashing Science funding, the Swiss are proposing to put it center stage on their currency. And I thought I was returning to the "Mecca of Science", not leaving it... 😅 Also, is this even real money? www.neuebanknotenserie.ch/detailview.h...

Beautifully controlled system to delineate primary from context-specific TF binding, revealing how chromatin state shapes TF binding specificity during differentiation and vice versa!

Excited to see that our study on context-specific transcription factors was named as one of 8 remarkable outputs of 2024 by the Swiss Institute of Bioinformatics.

The Range Extender For enhancers to function At long distances #ChromatinHaiku

Really cool work using a gene synteny-based strategy to identify enhancer conservation across species w/o seq similarity. Last figure is my favorite: while TFBS content is conserved, TFBS syntax is not! Aligns with our findings on TF cooperativity, where a specific syntax was not required.

As a scientist and mom of a little boy this story really touched me. The rewards of science funding go way beyond $ return on investment (& NIH's ROI is unparalleled). Hats off to the parents making this incredibly tough decision, paving the way for future treatments. www.nytimes.com/2025/05/15/h...

How is it end of April already? Excited to share that the Kribelbauer Lab is up and running @USC/MCB. Grateful for my first two PhD students @m-finegan.bsky.social @christinagirgis.bsky.social. We are dev scalable, genome-int. tools to study TF & enhancer regulation. Website now live bit.ly/4jo8Tjg

MPRAbase (mprabase.ucsf.edu) , a customized database for massively parallel reporter assays (MPRAs) to easily find and download MPRA data. Amazing work by Jingjing Zhao, Fotis Baltoumas, Georgios Pavlopoulos, @vagar.bsky.social, ilias Georgakopoulos-Soares & others. genome.cshlp.org/content/earl...

100% agree w Lowe on this: "But how is AGI going to suddenly reveal what is now hidden? The sum total of all the medical information in the world right now is not enough. And it's going to go on being Not Enough for quite some time..." Let's also focus on Exp. Tools! www.science.org/content/blog...

Looking for a Postdoc position in #Genomics at the interface of computational and molecular biology? -> The Rube lab at UC Merced is recruiting. I highly recommend you reach out! aprecruit.ucmerced.edu/JPF01874

Finally out! We present EXTRA-seq, a new EXTended Reporter Assay to quantify endogenous enhancer-promoter communication at kb scale! www.biorxiv.org/content/10.1... A 🧵about what it can do: #SynBio #DeepLearning #GeneRegulation

Neat study introducing a new system to study enhancer cooperativity across large distances in endogenous (!) contexts - showing that there is still much to learn about E-E and E-P communication. Enhancer order, distance, and strength, & CTCF sites all matter, and in a context-specific manner!

and here the flagship manuscript #Codebook

Curious to learn more about the Codebook Project? years-long, multi-center effort to identify binding specificities for poorly characterized human TFs. Read below if you want to learn more about 'dark' TFs (1/5 preprints in total).

(1/12) Excited to present the results of the large-scale benchmarking of DNA motif discovery tools using the Codebook data compendium on poorly studied human transcription factors and the Codebook Motif Explorer: dx.doi.org/10.1101/2024..., mex.autosome.org ⬇️.

(12/12) Kudos to the Codebook and GRECO-BIT consortium members including @bartdeplancke.bsky.social, see the whole team at ibis.autosome.org/docs/about_us

(1/8)📢Excited to announce the bioRxiv submission of my work from the past three years! Introducing meSMiLE-seq, a microfluidic assay aimed to understand how DNA modifications impact transcription factor (TF) binding, as part of the large Codebook/GRECO-BIT collab dx.doi.org/10.1101/2024... ✨🧵 ⬇️

looks like a great lineup!